Background: In children with intermediate-risk relapsed acute lymphoblastic leukemia (ALL), allogeneic hematopoietic stem cell transplantation (allo-HSCT) has markedly improved the outcome of patients with poor minimal residual disease (MRD) response. However, there is no consensus on the optimal conditioning regimen for allo-HSCT. Procedure: We prospectively analyzed the efficacy and safety of allo-HSCT with a unified conditioning regimen for children with intermediate-risk relapsed ALL, based on MRD in the bone marrow after induction, in the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) ALL-R08-II nationwide cohort. The conditioning regimen for allo-HSCT comprised total body irradiation (TBI), etoposide (ETP) and cyclophosphamide (CY) (UMIN000002025). Results: Twenty patients with post-induction MRD ≥ 10 ⁻³ and two with MRD that could not be evaluated underwent allo-HSCT. Engraftment was confirmed in all patients. No transplantation-related mortality was observed. The 3-year event-free survival and overall survival after transplantation were 86.4% ± 7.3% and 95.5% ± 4.4%, respectively. Conclusion: Allo-HSCT based on post-induction MRD with TBI + ETP + CY conditioning was highly effective and feasible for Japanese children with intermediate-risk relapsed ALL.